In a cooling system, such as for example a fluid chiller, e.g., water chiller, it may be desired to remove enough refrigerant out from the evaporator and out of contact with water tubes in the evaporator. This can avoid water tubes in the evaporator from freezing due to refrigerant migration from the evaporator to the condenser, such as at low ambient conditions. A pump down operation may be used to remove refrigerant out from the evaporator to address this problem, and the refrigerant is then stored for a period of time.